Reniform Nematode Genome Sequencing, Characterization, and Analysis

The reniform nematode (RN) is a devastating pest of cotton including over 300 plant genera thus, new methods are needed to control this organism. We have generated over 1.2 million genomic sequences, constituting 382 Mb of sequence data (5x coverage) using the new Roche GS-FLX titanium chemistry. A total of 67,317 contigs were obtained after assembly using GS De Novo Assembler. Overall assembled genome length range spanned over 37 Mb, or over 45%, of the expected total 80 Mb RN genome length. Fourteen types of repeats were identified in the RN genome, with majority of the 0.3% of the repeat content representing short stretches of low complexity regions or simple repeats. Total coding contigs predicted using Augustus gene prediction software were 20,457 (30.4%) of which 13,895 (20.6%) contigs did not have any Gene Ontology (GO) IDs. The highest GO distributions by molecular function, biological process, and cellular component were protein binding (32%), embryonic development (20%), and nuclear component (23%), respectively. Comparison of RN genome and Expressed Sequence Tags (ESTs) resulted in a total of 11,958 significant matches and thus assisting in validating majority of the gene predictions. The RN 18S rRNA major variants (RN_VAR1 and RN_VAR2) were represented in the assembled contigs. Nematode parasitism genes such as expansin b2, 14-3-3 protein, major sperm protein, glycosyl hydrolases family 31 protein, glutathione peroxidase, β-1,4-endoglucanase, and fmrfamide-related peptide flp-18 precursor were identified. These nematode parasitism genes will provide the necessary sequence data needed for investigating resistance against this organism.